Constructor Detail

• IntervalKeepPairFilter

  public IntervalKeepPairFilter​(List<Interval> intervals)

  Prepare to filter out SAMRecords that do not overlap the given list of intervals

  Parameters:

  intervals -

Method Detail

• filterOut

  public boolean filterOut​(SAMRecord record)

  Determines whether a SAMRecord matches this filter. Takes record, finds the location of its mate using the MC tag. Checks if either record overlaps the current interval using overlap detector. If yes, return false -> don't filter it out. If a read is secondary or supplementary, filter read out. Use IntervalFilter if you want to keep these reads, but NOTE: the resulting bam may not be valid.

  Specified by:

  filterOut in interface SamRecordFilter

  Parameters:

  record - the SAMRecord to evaluate

  Returns:

  true if the SAMRecord matches the filter, otherwise false

• filterOut

  public boolean filterOut​(SAMRecord first,
                           SAMRecord second)

  Determines whether a pair of SAMRecord matches this filter

  Specified by:

  filterOut in interface SamRecordFilter

  Parameters:

  first - the first SAMRecord to evaluate

  second - the second SAMRecord to evaluate

  Returns:

  true if both SAMRecords do not overlap the interval list